This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1qcg
From Proteopedia
(Difference between revisions)
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
==LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN== | ==LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN== | ||
| - | <StructureSection load='1qcg' size='340' side='right' caption='[[1qcg]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='1qcg' size='340' side='right'caption='[[1qcg]], [[Resolution|resolution]] 2.10Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1qcg]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1qcg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_americana Phytolacca americana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCG FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcg OCA], [https://pdbe.org/1qcg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qcg RCSB], [https://www.ebi.ac.uk/pdbsum/1qcg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcg ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/RIP1_PHYAM RIP1_PHYAM] Inhibits viral infection of plants, and protein synthesis in vitro. |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 19: | Line 19: | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qcg ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qcg ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The pokeweed antiviral protein (PAP) belongs to a family of ribosome-inactivating proteins (RIP), which depurinate ribosomal RNA through their site-specific N-glycosidase activity. We report low temperature, three-dimensional structures of PAP co-crystallized with adenyl-guanosine (ApG) and adenyl-cytosine-cytosine (ApCpC). Crystal structures of 2.0-2.1 A resolution revealed that both ApG or ApCpC nucleotides are cleaved by PAP, leaving only the adenine base clearly visible in the active site pocket of PAP. ApCpC does not resemble any known natural substrate for any ribosome-inactivating proteins and its cleavage by PAP provides unprecedented evidence for a broad spectrum N-glycosidase activity of PAP toward adenine-containing single stranded RNA. We also report the analysis of a 2.1 A crystal structure of PAP complexed with the RIP inhibitor pteoric acid. The pterin ring is strongly bound in the active site, forming four hydrogen bonds with active site residues and one hydrogen bond with the coordinated water molecule. The second 180 degrees rotation conformation of pterin ring can form only three hydrogen bonds in the active site and is less energetically favorable. The benzoate moiety is parallel to the protein surface of PAP and forms only one hydrogen bond with the guanido group of Arg135. | ||
| - | + | ==See Also== | |
| - | + | *[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Phytolacca americana]] | [[Category: Phytolacca americana]] | ||
| - | [[Category: Irvin | + | [[Category: Irvin JD]] |
| - | [[Category: Kurinov | + | [[Category: Kurinov IV]] |
| - | [[Category: Myers | + | [[Category: Myers DE]] |
| - | [[Category: Uckun | + | [[Category: Uckun FM]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN
| |||||||||||
